Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	41.3%	54.6 / 23.9	47	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (19/8);  new base T (0/19);  total (19/28)
Fisher's exact test for biased strand distribution p-value = 5.49e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGC  >  NC_000913/357729‑358017                                                                                                                                                        |                                                                                                                                                   aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTAtttt                                                                                                                                                <  1:477164/151‑1 (MQ=255) aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCACCCCCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTAtttt                                                                                                                                                <  1:613264/151‑1 (MQ=255)       tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑ccgcc                                                                                                                                         >  1:21125/1‑151 (MQ=255)        aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑ccgcc                                                                                                                                         <  2:71479/150‑1 (MQ=255)             tgatgaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑Gcaac                                                                                                                                   >  2:9206/1‑150 (MQ=255)             tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑Gcaac                                                                                                                                   >  1:973613/1‑150 (MQ=255)               aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTCCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACaaa                                                                                                                                <  1:698420/151‑1 (MQ=255)                 aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAAc                                                                                                                              <  2:1119919/151‑1 (MQ=255)                    cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAAccgc                                                                                                                           <  2:1190560/151‑1 (MQ=255)                          gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTtct                                                                                                                     >  2:994576/1‑151 (MQ=255)                          gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTtct                                                                                                                     >  2:215575/1‑151 (MQ=255)                           cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTtctc                                                                                                                    >  2:430983/1‑151 (MQ=255)                            aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCA‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGGtct                                                                                                                     >  1:61430/1‑149 (MQ=255)                               aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAAACG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTcc                                                                                                                 >  2:449522/1‑150 (MQ=255)                                    aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                           >  1:1180567/1‑151 (MQ=255)                                      tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                         >  2:412255/1‑151 (MQ=255)                                              cagcccttgtccAGCGGCT‑CCGTGATTTCTTTCCCCCC‑AACACCCC‑CCAATTTACCCACCCCCAGGTAAAAAAATC‑CCTCGGCGGGGGTTG‑TCTGCCAGTTTTTTTC‑CCCCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                   <  2:798146/138‑1 (MQ=255)                                                       tccAGCGCCTCCCGTGT‑TTCTTCCCCCCC‑AACACCCG‑CTCTTTTCCCCACCGCAATGT‑CAAAAATT‑CCCTCGGGGGCGGTT‑TCCGCCCGGTTTTTTTCCCGCC‑ACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑Gaaa                                                                                          <  1:1092899/146‑1 (MQ=255)                                                               gcctcccttatttctttCCCCC‑AAACACCGCCGCATTTCCCCACCGCAATGTGAAAAATTC‑CCTTGGGGGC‑GCTGTTCTCCAAGTTTTTTCC‑CCGCC‑AAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTaa                                                                                <  1:635475/137‑1 (MQ=255)                                                               cTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGgaaa‑gaaaaaagttt                                                                                   >  2:115766/1‑140 (MQ=25)                                                                  ccGTAA‑TTCATTCCCGCC‑AACACCCG‑CTCTTTTACCCACCGCCATGTGAAAAAATC‑CCTCCGGGGCGGCTT‑TCGGCCAGCTTTTTTC‑CCGCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCg                                                                           <  2:837788/151‑1 (MQ=255)                                                                   cggggtttCATTCCCCCC‑AACACCCC‑CGCTTTTACCAACCCCCATGTCCAAAAATC‑CCTCCGGGGCGGCTG‑TCGCCCAGCTTTTTTT‑CCCCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑tt                                                                                   <  2:425523/137‑1 (MQ=255)                                                                   cccttttttctttCCCCCAAACACCCC‑CGCTTTCATCCACCCCTGTGTACAAAAATC‑CCTCCGCGGGGTTTG‑TCGCCCGGCTTTTTTC‑CCCCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGcc                                                                             <  1:522690/140‑1 (MQ=255)                                                                              ttcccccaaacaccCG‑CGCTTTTACCCAACCCAATTTAAAAAAACG‑CCTCCGGGGCGCTTG‑TCTCCCGTTTTTTTTC‑CCGCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCAt                                                                       <  2:1080253/137‑1 (MQ=255)                                                                              ttcccccaaacaccCG‑CGCATTTACCCACCCCCTTGTGAAAAAATC‑CCTTCGGGGGGGCTG‑TCTGCCATTTTTTTTC‑CCGCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCAtgt                                                                     <  2:592815/139‑1 (MQ=255)                                                                                ccGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGGAAAAACA‑TTTAACCCCgcatttt                                                                     >  2:1092883/1‑139 (MQ=25)                                                                                  gCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAAAAAC‑TTTTAAccccgccttttgt                                                                  >  2:210405/1‑135 (MQ=25)                                                                                        caacCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GAAAAAACATTTAAACCC‑CCCTGTTGTGTGGGGATCg                                                        >  2:894792/1‑150 (MQ=25)                                                                                           acccgcgaTTTACCCAACCCCATTGTCAAAAACGCCCTCCGGGGGGGTTG‑TTTGCGACTTTTTTGC‑CCCCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                      <  2:906168/144‑1 (MQ=255)                                                                                               cgcTTTTACCCACCGCCGTGTAAAAAAATG‑CCTCCGGGGCGGCTG‑TCTCCCATTTTTTTTC‑CCGCC‑AAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg                                                  <  1:237831/150‑1 (MQ=255)                                                                                               cgcTTTTACCCACCCCCATGGAAAAAAAGC‑CCTCCGGGGCGGCTG‑TCGCCCAGTTTTTTTC‑CCCCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                   <  2:1134696/149‑1 (MQ=255)                                                                                                          aaCGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAAAA‑TTTAA‑CCCCCCCTGGTGTGTGGGGGTCGCCGCTGGtgaaaa                                           >  1:1047196/1‑141 (MQ=21)                                                                                                           aCGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAA‑GGAAAAAC‑TTTTAAACCCTCCCCTTGTGTGGGGATCACTGCTGGGATCAAagt                                        >  2:1026687/1‑148 (MQ=19)                                                                                                           aCGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGG‑GGAAAAAA‑TTTAAATCCGCCCACTTGTGTGGGGAACGCTGCTgggtaaaaaat                                        >  1:759344/1‑139 (MQ=19)                                                                                                            cGCCTTGTGAAAAAAGG‑CCTTCGCGGCGGTTG‑TCTGCCAGTTTTTTTC‑CCGCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                    <  2:87521/151‑1 (MQ=255)                                                                                                              ccATGGGAAAAAATG‑CTGCGGCGGCGGCTG‑TC‑CCCAGTTTTTTTTCCCCCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                  <  1:486005/151‑1 (MQ=255)                                                                                                                cttgagcaaaaTGCCCTCCGCGCGGGCTG‑TCGCCCAGCT‑TTTTT‑CCGCCGGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaaa                                   <  2:238497/142‑1 (MQ=255)                                                                                                                   tgCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGGCGGA‑GAAAAAAC‑ATTTATCCCCCCACCTTTTGTGGGGATCGCCGCTGGTGACaaaaagg                                      >  1:884031/1‑137 (MQ=255)                                                                                                                      aaaaaTC‑CCTTCGCGGCGGCTT‑TCTCCCAGTTTTTTTC‑CCGCC‑CCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                            <  1:889339/149‑1 (MQ=255)                                                                                                                        aaaagcccTCCGCGGCGGCTG‑TCGGCCGGCTATTTTC‑CCGCC‑ACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                         <  2:1133552/145‑1 (MQ=255)                                                                                                                         aaTG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGA‑GGAAAAAG‑TTTAAACCCCCCCTGTTTGGGGGGAATCACCGCTGGTGAAAAATTGGGAAggggggggggg                        >  1:1180884/1‑142 (MQ=255)                                                                                                                              ccTTCGCGGGGCCGG‑TCTCCCAGCTTTTTTC‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                   <  2:973643/151‑1 (MQ=255)                                                                                                                                   ggggggccTG‑TCTCCCAGTTTTTTTC‑CCCCC‑ACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                 <  2:1007016/141‑1 (MQ=255)                                                                                                                                     ggcggcTG‑TCTGCCAGTTTTTTTC‑CCCCC‑GAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                 <  2:362243/146‑1 (MQ=255)                                                                                                                                         gttG‑TCGGCCACCTTTTTTC‑CCCCC‑ACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg          <  2:1175515/147‑1 (MQ=255)                                                                                                                                            tttcgcccAGTTTTTTTC‑CCGCC‑GCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa        <  2:1179468/143‑1 (MQ=255)                                                                                                                                                  ccAGTTATTTTC‑CCGCC‑GCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc  <  1:693054/149‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                   AACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCC‑AACAACCG‑CGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCC‑GCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGC  >  NC_000913/357729‑358017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑